Congenital Disorders of Glycosylation Panel

Last modified: Jun 12, 2018

Summary

  • Is a 47 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of a congenital disorder of N-linked glycosylation or combined defects of glycosylation affecting both the N-linked and O-linked glycosylation pathways. The genes on this panel are included in the Comprehensive Metabolism Panel.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

47

Test code

ME1901

CPT codes

SEQ 81406
DEL/DUP 81479
SEQ 81479

Summary

The Blueprint Genetics Congenital Disorders of Glycosylation Panel (test code ME1901):

  • Is a 47 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Congenital Disorders of Glycosylation Panel

ICD-10 Disease
E77.9 Disorder of glycoprotein metabolism

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Most subtypes of congenital disorders of glycosylation (CDG) are classified as disorders of N-glycosylation, which involves carbohydrates called N-linked oligosaccharides. These oligosaccharides are created in a specific order to create specific sugar trees, which are then attached to proteins on various cells. Disorders of N-glycosylation are due to an enzyme deficiency or other malfunction somewhere along the N-glycosylation pathway. There are 42 different enzymes in the pathway; any of them may be mutated and cause a disorder belonging to this group. Different mutated enzymes cause different phenotypes. Congenital disorders of N-linked glycosylation are a genetically and phenotypically heterogeneous group of diseases. Most commonly, symptoms begin in early infancy. Manifestations range from mild to severe, involving only protein-losing enteropathy and hypoglycemia or severe intellectual disability with malfunction of several organs. Sometimes the disorder may be fatal. Most patients require nutritional supplements. Most of the individual disorders have been observed only in a very limited number of patients. The most common ones are PMM2-related disorder (approximately 700 patients reported), MPI-related disorder (>20 patients) and ALG6-related disorder (>30 patients). Other types of disorder are extremely rare. In addition to congenital disorders of N-linked glycosylation, this panel has the ability to diagnose rare phenotypes with overlapping symptoms such as GEN-related myopathy and ATP6V0A2- related cutis laxa. The panel also covers genes for CDG that occur due to combined defects of glycosylation; defects affecting both the N-linked and O-linked glycosylation pathways. Genes for disorders of protein O-glycosylation, which in many cases have been classified as subtypes of other umbrella groups (e.g., muscular dystrophy), and show more dysmorphic features in general, are better known with more traditional names and can be found on other panels.

Genes in the Congenital Disorders of Glycosylation Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ALG1* Congenital disorder of glycosylation AR 23 43
ALG2 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 4 5
ALG3 Congenital disorder of glycosylation AR 9 17
ALG6 Congenital disorder of glycosylation AR 8 24
ALG8 Congenital disorder of glycosylation AR 10 17
ALG9 Congenital disorder of glycosylation, Gillessen-Kaesbach-Nishimura syndrome AR 4 4
ALG11* Congenital disorder of glycosylation AR 11 14
ALG12 Congenital disorder of glycosylation AR 10 15
ALG13 Congenital disorder of glycosylation XL 5 9
ATP6V0A2 Cutis laxa, Wrinkly skin syndrome AR 16 54
B3GLCT Peters-plus syndrome AR 9 15
B4GALT1 Congenital disorder of glycosylation AR 1 2
COG1 Congenital disorder of glycosylation AR 4 2
COG4 Congenital disorder of glycosylation AR 9 4
COG5 Congenital disorder of glycosylation AR 3 10
COG6 Congenital disorder of glycosylation, Shaheen syndrome AR 9 9
COG7 Congenital disorder of glycosylation AR 5 5
COG8 Congenital disorder of glycosylation AR 5 7
DDOST Congenital disorder of glycosylation AR 3 2
DHDDS Retinitis pigmentosa AR 4 7
DOLK Congenital disorder of glycosylation AR 8 11
DPAGT1 Congenital disorder of glycosylation, Myasthenic syndrome, congenital AR 17 30
DPM1 Congenital disorder of glycosylation AR 8 8
DPM2 Congenital disorder of glycosylation AR 2 2
DPM3 Congenital disorder of glycosylation AR 2 2
GMPPA Alacrima, achalasia, and mental retardation syndrome AR 6 11
GNE Inclusion body myopathy, Nonaka myopathy, Sialuria AD/AR 58 201
MAGT1 Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia, Mental retardation, X-linked 95 XL 5 14
MAN1B1 Mental retardation AR 8 25
MGAT2 Congenital disorder of glycosylation AR 6 5
MOGS Congenital disorder of glycosylation AR 6 6
MPDU1 Congenital disorder of glycosylation AR 6 7
MPI Congenital disorder of glycosylation AR 17 19
NGLY1 Congenital disorder of deglycosylation AR 24 22
PGM1 Congenital disorder of glycosylation AR 10 30
PMM2 Congenital disorder of glycosylation AR 62 127
RFT1 Congenital disorder of glycosylation AR 10 10
SEC23B Anemia, dyserythropoietic congenital AR 15 120
SLC35A1 Congenital disorder of glycosylation AR 4 4
SLC35A2 Congenital disorder of glycosylation XL 15 15
SLC35C1 Congenital disorder of glycosylation, Leukocyte adhesion deficiency AR 6 7
SRD5A3* Kahrizi syndrome, Congenital disorder of glycosylation AR 13 16
SSR4 Congenital disorder of glycosylation XL 5 6
STT3A Congenital disorder of glycosylation AR 1 1
STT3B Congenital disorder of glycosylation AR 1 2
TMEM165 Congenital disorder of glycosylation AR 4 6
TUSC3 Mental retardation AR 4 14

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ALG6 Chr1:63871975 c.347-13C>G NM_013339.3
COG5 Chr7:106898843 c.1669-15A>G NM_006348.3
COG6 Chr13:40273614 c.1167-24A>G NM_020751.2 rs730882236
DHDDS Chr1:26774026 c.441-24A>G NM_024887.3 rs764831063
PGM1 Chr1:64113966 c.1199-222G>T NM_001172818.1
PGM1 Chr1:64124734 c.1654-523G>A NM_001172818.1
PMM2 Chr16:8898599 c.179-25A>G NM_000303.2 rs760689221
PMM2 Chr16:8941558 c.640-23A>G NM_000303.2
SEC23B Chr20:18488615 c.-16A>G NM_006363.4
SEC23B Chr20:18488060 c.-571A>G NM_006363.4 rs559854357
SEC23B Chr20:18526845 c.1743+168A>G NM_006363.4 rs111951711
SEC23B Chr20:18491863 c.221+163A>G NM_006363.4 rs573898514
SEC23B Chr20:18491731 c.221+31A>G NM_006363.4
SEC23B Chr20:18492791 c.222-78C>T NM_006363.4 rs150393520
STT3B Chr3:31663820 c.1539+20G>T NM_178862.1
TMEM165 Chr4:56284334 c.792+182G>A NM_018475.4 rs793888506

Added and removed genes from the panel

Genes added Genes removed
NGLY1
RPN2

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics congenital disorders of glycosylation panel covers classical genes associated with disorder of glycoprotein metabolism, GEN-related myopathy and ATP6V0A2-related cutis laxa. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.